From a0a7efed1e683644dae2f88cffbc531c3b7aa8a3 Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Wed, 14 Mar 2018 23:22:06 +0100
Subject: [PATCH] EOD

---
 R/install_beast2.R                         |  2 +-
 R/is_beast2_input_file.R                   | 24 ++++++++++++++++++----
 man/is_beast2_input_file.Rd                |  4 +++-
 tests/testthat/test-is_beast2_input_file.R | 22 ++++++++++++++++++++
 4 files changed, 46 insertions(+), 6 deletions(-)

diff --git a/R/install_beast2.R b/R/install_beast2.R
index 1c7662a..209a69c 100644
--- a/R/install_beast2.R
+++ b/R/install_beast2.R
@@ -11,7 +11,7 @@
 #' @note This function only tested to work under GNU/Linux
 #' @export
 install_beast2 <- function(folder_name) {
-  dir.create(path = folder_name, recursive = TRUE)
+  dir.create(path = folder_name,  showWarnings = FALSE, recursive = TRUE)
   tgz_filename <- "BEAST.v2.4.7.Linux.tgz"
   url <- paste0(
     "https://github.com/CompEvol/beast2/releases/download/v2.4.7/",
diff --git a/R/is_beast2_input_file.R b/R/is_beast2_input_file.R
index 2439ff1..8ee0520 100644
--- a/R/is_beast2_input_file.R
+++ b/R/is_beast2_input_file.R
@@ -4,12 +4,14 @@
 #' @param beast2_jar_path the path of \code{beast.jar}.
 #'   Use \link{get_default_beast2_jar_path} to get
 #'   the default BEAST jar file's path
+#' @param show_warnings if TRUE, warnings will shown
 #' @return TRUE if the file is valid, FALSE if not
 #' @author Richel J.C. Bilderbeek
 #' @seealso Use \code{\link{are_beast2_input_lines}} to check the lines
 #' @export
 is_beast2_input_file <- function(
   filename,
+  show_warnings = FALSE,
   verbose = FALSE,
   beast2_jar_path = get_default_beast2_jar_path()
 ) {
@@ -37,14 +39,28 @@ is_beast2_input_file <- function(
   # An error code of 0 denotes that the file was valid
   status_code <- system(cmd, ignore.stderr = TRUE, ignore.stdout = TRUE)
 
-  # Valid BEAST2 input files will result in an output with 'Done!' at the
-  # last line
-  output <- system(cmd, intern = TRUE, ignore.stderr = TRUE)
-
+  cmds <- unlist(strsplit(x = cmd, split = " "))
+  output <- system2(
+    cmds[1],
+    args = cmds[2:length(cmds)],
+    stdout = TRUE,
+    stderr = TRUE
+  )
   if (verbose) {
     print(output)
   }
 
+  if (show_warnings == TRUE &&
+      sum(grepl(x = output, pattern = "WARNING: "))) {
+    warning(output[grepl(x = output, pattern = "WARNING: ")])
+  }
+
+  if (1 == 2) {
+    # Valid BEAST2 input files will result in an output with 'Done!' at the
+    # last line
+    output <- system(cmd, intern = TRUE, ignore.stderr = TRUE)
+  }
+
   # Invalid files are not valid BEAST2 input files
   # Create an if statement here,
   # if there is an input file that violates this assert,
diff --git a/man/is_beast2_input_file.Rd b/man/is_beast2_input_file.Rd
index d615be5..dc5c345 100644
--- a/man/is_beast2_input_file.Rd
+++ b/man/is_beast2_input_file.Rd
@@ -4,12 +4,14 @@
 \alias{is_beast2_input_file}
 \title{Is a file a valid BEAST2 input file?}
 \usage{
-is_beast2_input_file(filename, verbose = FALSE,
+is_beast2_input_file(filename, show_warnings = FALSE, verbose = FALSE,
   beast2_jar_path = get_default_beast2_jar_path())
 }
 \arguments{
 \item{filename}{name of the BEAST2 XML input file}
 
+\item{show_warnings}{if TRUE, warnings will shown}
+
 \item{verbose}{if TRUE, additional information is displayed, that
 is potentially useful in debugging}
 
diff --git a/tests/testthat/test-is_beast2_input_file.R b/tests/testthat/test-is_beast2_input_file.R
index 0dd226b..ad56056 100644
--- a/tests/testthat/test-is_beast2_input_file.R
+++ b/tests/testthat/test-is_beast2_input_file.R
@@ -58,3 +58,25 @@ test_that("abuse", {
   )
 
 })
+
+test_that("detect warnings", {
+
+  testthat::expect_warning(
+    is_beast2_input_file(
+      filename = beastier:::get_beastier_path("beast2_warning.xml"),
+      show_warnings = TRUE
+    )
+  )
+  testthat::expect_silent(
+    is_beast2_input_file(
+      filename = beastier:::get_beastier_path("beast2_warning.xml"),
+      show_warnings = FALSE
+    )
+  )
+  testthat::expect_silent(
+    is_beast2_input_file(
+      beautier:::get_beautier_paths("2_4.xml"),
+      show_warnings = TRUE
+    )
+  )
+})